Align asparagine-oxo-acid transaminase (EC 2.6.1.14); alanine-glyoxylate transaminase (EC 2.6.1.44); serine-glyoxylate transaminase (EC 2.6.1.45) (characterized)
to candidate WP_089323238.1 CHB58_RS06165 alanine--glyoxylate aminotransferase family protein
Query= BRENDA::Q56YA5 (401 letters) >NCBI__GCF_900188395.1:WP_089323238.1 Length = 392 Score = 224 bits (570), Expect = 4e-63 Identities = 137/393 (34%), Positives = 213/393 (54%), Gaps = 12/393 (3%) Query: 7 PGRHHLFVPGPVNIPEPVIRAMNRNNEDYRSPAIPALTKTLLEDVKKIFKTTSGTPFLFP 66 P + L PGP +PE V++AM + +RSP + +E +K++FKT T + Sbjct: 3 PLKERLMTPGPTPVPERVLQAMASHTMYHRSPKFKEIFAETIERLKRLFKTERDT-LILT 61 Query: 67 TTGTGAWESALTNTLSPGDRIVSFLIGQFSLLWIDQQKRLNFNVDVVESDWGQGANLQVL 126 ++GTGA E+A++N SPGD V + G+F W + + N V+E +WG+ N + + Sbjct: 62 SSGTGAMEAAVSNLFSPGDSAVVIVGGKFGQRWKELCETFGVNPVVIELEWGKSVNPEDV 121 Query: 127 ASKLSQDENHTIKAICIVHNETATGVTNDISAVRTLLDHYKHPALLLVDGVSSICALDFR 186 K+ +EN IK + + ET+TG ND+ A+ + Y + +L+ DG+++ D Sbjct: 122 KKKI--EENRNIKGVLVQICETSTGAFNDVKALGEITARYDN-VILVADGITAFGVYDIP 178 Query: 187 MDEWGVDVALTGSQKALSLPTGLGIVCASPKALEATKTSKSLKVFFDWNDYLKFYKLGTY 246 +D+W +DVA+TGSQKAL P GL ++ S KA ++ + K +FD + +K G Sbjct: 179 VDDWNIDVAITGSQKALMTPPGLAVISLSEKA-KSRLSRKKWAYYFDLSKEIKNQAKG-Q 236 Query: 247 WPYTPSIQLLYGLRAALDLIFEEGLENIIARHARLGKATRLAVEAWGLKNCTQKEEWISN 306 YTP++ L+ GL AL +I EEGLEN+ RH L K+ R ++A L+ E +N Sbjct: 237 TAYTPAVNLIVGLNEALKMIEEEGLENVAKRHEILAKSARAGIKALELE---LLPEHPAN 293 Query: 307 TVTAVMVPPHIDGSEIVRRAWQRYNLSLGLGLNKVAGKVFRIGHLGNVNELQLLGCLAGV 366 VTAV +P HIDG + V R + + G + GK+FR+ H+G ++ LL L V Sbjct: 294 GVTAVKLPEHIDGQKFVSWIRDRLGIVIAGGQEHLKGKIFRLSHMGYIDIFDLLTQLEAV 353 Query: 367 EMILKDVGYPVVMGSGVAAA-STYLQ--HHIPL 396 E L + G VAAA TY++ H P+ Sbjct: 354 EFALTRMEMYPAYGKAVAAAMETYIELVHQSPI 386 Lambda K H 0.320 0.137 0.419 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 356 Number of extensions: 14 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 401 Length of database: 392 Length adjustment: 31 Effective length of query: 370 Effective length of database: 361 Effective search space: 133570 Effective search space used: 133570 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory